This should be a pretty simple job. First you'll need your 120mm fan. A grill and filter will be up to you. A filter will help with dust but if you clean you rig on a semi-regular basis its not really a must have. The grill would be to keep things out of the fan (your fingers...). If you havent gotten the fan already just pick up a grill at the same time.
As for the drilling, your gonna need a hole saw. Only problem will be finding a 4.7" (120mm) hole saw. You next best bet would be to make a hole jig and use a dremel or like tool to fashion the hole. A a third option you could make a templet of the hole and follow the edges with a dremel. It will be a bit tricky but you want to take your time some that you have a perfectly round and smooth hole.
When you actually begin cutting you should cover the plexi on both sides with masking tape to prevent scratching and chipping. Also be careful on using too much pressure as plexi will fracture when cutting if your not careful. Once you get done with the hole you will need the chamfer the edge to ensure that the edges arnt sharp as this is where most cracks begin in plexiglass.
then all you have to do is line the fan up, mark the screw holes and drill them. Again being careful with the pressure.
Hope this helps